This application relates to the testing of DNA from a patient sample for mutations, and more particularly to testing for mutations associated with cancer or other diseases for use in diagnosis and targeted screening.
It is becoming increasingly clear that many diseases are caused by genetic mutations. In some cases, these mutations are inherited. In others the mutations are acquired during the lifetime of the individual, for example as a result of exposure to radiation or carcinogenic chemicals. Early diagnosis and optimal treatment of diseases resulting from such mutations will often depend on the ability to detect the mutation, and in some cases to detect the specific nature of the mutation. To this end, various methods have been developed for testing for genetic mutations.
One class of tests makes use of immunodiagnostic techniques such as ELISA to detect the presence or absence of a protein product of the diagnostically important gene. Such tests make use of an antibody which selectively binds to either the normal protein product of the gene or the protein product of the mutated gene, and detect the presence or absence of binding. These tests are generally relatively low in cost. They suffer, however, from low clinical accuracy because they produce many false negative results. This has led workers in the field to question the value of immunodiagnostic tests for diagnosis of or screening for genetic diseases. See Beebe et al., J. Clin. Microbiol. 31: 2535-7 (1993); Warren, et al., J. Clin. Microbiol. 31:1663-6 (1993); Roberts et al., The Lancet 336:1523 (1990); De Cresce et al., Medical Laboratory Observer 25:28 (1993); Einstein et al., New Engl. J. Med. 322:178-183 (1990); Hall P. A., J Pathology 172:1-4 (1994).
A second class of tests for identifying gene mutations in patient samples makes use of nucleic acid probes which specifically hybridize with the portion of the gene containing the mutation site. Probe-based tests have high accuracy (few false negatives) and specificity (few false positives) for the specific mutation. A drawback to probe-based tests, however, is this very specificity which requires a priori detailed knowledge of the mutation being tested for, requires a unique set of reagents for each mutation, and may result in the failure to detect new types of mutations. Because of these drawbacks, this class of tests has also been criticized by some as being inadequate for meeting the diagnostic and screening challenges of the future. Ewanowich et al., J. Clin. Microbiol. 31:1715-25 (1993); Hatcher et al., Prenat. Diagn. 13:171-7 (1993); Bull et al., The Lancet 340:1360 (1992).
A third class of tests obtains the full sequence of the DNA for a particular gene recovered from the sample. Erickson, D., Scientific American 267:116 (1992). Rather than infer a diagnosis from indirect probe or protein tests, these tests read the DNA sequence of the gene of interest base by base. This method, which is known as Sequence-Based Diagnosis or SBD has the advantage of near 100% accuracy and 100 specificity. The disadvantage of this method, however, is the cost (approximately $1.00 per base) which effectively renders the method unavailable for screening applications, and even for many diagnostic applications.
It is an object of the present invention to provide a method for testing for mutations in DNA from a patient sample that meets the challenge of providing accurate, specific and yet cost effective diagnosis and targeted screening for the ever growing number of diseases associated with mutations in the genetic code.